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We need the ability to create OpenMM `System` objects with context parameters that allow us to perform relative free energy calculations between two `System` endpoints.
We presume that the user start…
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### Bug summary
Hi everyone,
I am trying to run gmx_MMPBSA on a DNA-aptamer-ligand trajectory obtained in Gromacs using the CHARMM ff. I successfully ran the calculations using the complex trajec…
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I just realized we could include the [anisotropic long-range dispersion correction](http://pubs.acs.org/doi/abs/10.1021/jp0735987) in a very simple and inexpensive way via HMC: When we run the dynamic…
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Hello.
Thanks for this awesome work.
This is related to #72 and #98
I am trying to understand if I can use transformato for a protein-peptide system where there are point mutations in the peptide(…
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Dear all,
When I generate poses as so:
```
vina --ligand ligand.pdbqt --receptor receptor_rigid.pdbqt --flex receptor_flex.pdbqt --out global_search.pdbqt --cpu 8 --size_x 22.5 --size_y 22.5 --si…
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(Links below will open the PDF with the Google Docs viewer. Default GitHub behavior would be to download the file instead.)
**Article file diff**, using `latexdiff`
[revised_manuscript_marked_up.…
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**In broad terms, what are you trying to do?**
Calculate binding free energies using expanded ensemble simulations, AWH, or potentially simple "array of lambda" simulations. Hamiltonian replic…
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I wonder if I can have an example of the format of the symmetrize block, please? Thanks.
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geom_labelvline and geom_labelhline are very useful tools for setting baselines/thresholds and annotating them. In the case of the vertical line options it seems like it would be appealing to be able …
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### Type of project
Building a plug-in for Impact Framework
### Overview
## Background
The energy consumption of blockchain is a growing concern. Currently, according to some researches, *…
ktg9 updated
5 months ago